Molecular-orbital study of the relative stability of protonated nucleic acid base pairs

Abstract

Molecular-orbital MNDO/M calculations of various purine-pyrimidine complexes were carried out to study the effect of nucleic acid base protonation on the relative stability of their complementary and non-complementary pairs. The protonation of one of the bases was shown to produce considerable changes in the formation energy and structure of these complexes. The protonation of the 06, N3 and N7 atoms in guanine increases the relative stability of their complementary pair, whereas the protonation of N3 or N7 of adenine and O2 or O4 of uracil decreases the energy difference for the formation of matched and mismatched complexes. Very high stability was observed for the non-complementary pair A (N1)+C, in which adenine is protonated at the N1 site, and the mismatched pair AC + (O2). Show more